--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Scan_IUPAC_output_each_match.pl	Mon Apr 09 04:45:06 2018 -0400
@@ -0,0 +1,210 @@
+#! /usr/bin/perl
+
+use strict;
+use FileHandle;
+use Bio::SeqIO;
+#use Statistics::Descriptive;
+
+#####
+# Program to count all occurences of a particular REGEX 
+# in a file containing mutiple FASTA sequences.
+# 11 September 2003. Ian Donaldson.
+# Revised to convert IUPAC to regex
+# Revised to read a multiple FASTA file
+# was CountRegexGFF_IUPAC_1input_nosummary.pl
+#####
+
+#### File handles
+my $input = new FileHandle;
+my $output = new FileHandle;
+
+#### Variables
+my $file_number = 0;
+my $count_fwd_regex = 0;
+my $count_rvs_regex = 0;
+my $count_all_regex = 0;
+my $seq_tally = 0;
+my @seq_totals = ();
+
+#### Command line usage
+if(@ARGV != 5) {
+   die ("USAGE: 
+   $0
+   IUPAC
+   Multiple FASTA input file
+   Output
+   Label
+   Skip palindromic (0=F+R-default|1=F only)\n\n");
+} 
+
+#### Search forward strand only?
+my $skip = $ARGV[4];
+unless($skip =~ /^[01]$/) {
+   die("Only accept 0 or 1 for Skip!\n");
+}
+
+#### Process IUPAC string
+my $iupac = $ARGV[0];
+chomp $iupac;
+$iupac = uc($iupac);
+
+if($iupac !~ /^[ACGTRYMKWSBDHVN]+$/) {
+   die("A non-IUPAC character was detected in your input string!\n");
+}
+
+#### Forward strand IUPAC
+my @fwd_iupac_letters = split(//, $iupac); 
+my @fwd_regex_list = ();
+
+foreach my $letter (@fwd_iupac_letters) {
+   my $converted_iupac = iupac2regex($letter);
+   push(@fwd_regex_list, $converted_iupac);
+}
+
+my $fwd_regex = join('', @fwd_regex_list);
+
+
+#### Reverse strand IUPAC
+my $revcomp_iupac = RevCompIUPAC($iupac);
+my @rev_iupac_letters = split(//, $revcomp_iupac); 
+my @rev_regex_list = ();
+
+foreach my $letter (@rev_iupac_letters) {
+   my $converted_iupac = iupac2regex($letter);
+   push(@rev_regex_list, $converted_iupac);
+}
+
+my $rvs_regex = join('', @rev_regex_list);
+
+#### Other variables
+my $label = $ARGV[3]; 
+
+if($label !~ /^[\w\d]+$/) {
+   die("A non-letter/number character was detected in your label string!\n");
+}
+
+my $length = length($iupac);
+
+#### Open output file
+$output->open(">$ARGV[2]") or die "Could not open output file $ARGV[2]!\n";
+#$output->print("##gff-version 2\n");
+
+#if($skip == 0) {
+#   $output->print("##Pattern search: $iupac and $revcomp_iupac\n");
+#}
+
+#else {
+#   $output->print("##Pattern search: $iupac\n");
+#}
+
+#### Work thru FASTA entries in the input file with SeqIO
+my $seqio = Bio::SeqIO->new(-file => "$ARGV[1]" , '-format' => 'Fasta');
+
+while( my $seqobj = $seqio->next_seq() ) {
+   $seq_tally++;
+   my $this_seq_tally = 0;
+   my $sequence = $seqobj->seq(); # actual sequence as a string
+   my $seq_id = $seqobj->id(); # header
+   #print(">$seq_id\n$seq\n\n");
+
+   #$output->print(">$seq_id\n");
+
+   #### Clean up $sequence to leave only nucleotides
+   $sequence =~ s/[\s\W\d]//g;
+
+   while ($sequence =~ /($fwd_regex)/ig) {
+      $this_seq_tally++;
+      $count_fwd_regex++; 
+      $count_all_regex++;
+      
+      my $end_position = pos($sequence);
+      my $start_position = $end_position - ($length - 1);
+      $output->print("$seq_id\tRegexSearch\tCNS\t$start_position\t$end_position\t.\t+\t.\t$label\n"); 
+   }
+
+   #### Count reverse REGEX
+   unless($skip == 1) {
+      while ($sequence =~ /($rvs_regex)/ig) {
+         $this_seq_tally++;
+         $count_rvs_regex++;
+         $count_all_regex++;
+
+         my $end_position = pos($sequence);
+         my $start_position = $end_position - ($length - 1);
+         $output->print("$seq_id\tRegexSearch\tCNS\t$start_position\t$end_position\t.\t-\t.\t$label\n"); 
+      }
+
+   push(@seq_totals, $this_seq_tally);
+   #$output->print("$this_seq_tally matches\n");
+   }
+}
+
+#### Mean motifs per seq
+#my $stat = Statistics::Descriptive::Full->new();
+#$stat->add_data(@seq_totals); 
+#my $mean = $stat->mean();
+
+
+#### Print a summary file
+if($skip == 0) {
+#   $output->print("##Forward: $fwd_regex. Reverse: $rvs_regex.\n",
+#                  "##$count_fwd_regex on the forward strand.\n",
+#                  "##$count_rvs_regex on the reverse strand.\n",
+#                  "##$count_all_regex in total.\n",
+#                  "##$seq_tally sequences.  Mean motifs per seq = $mean\n");
+#
+   print STDOUT "There were $count_all_regex instances of $fwd_regex and $rvs_regex.\n"; 
+}
+
+if($skip == 1) {
+#   $output->print("##Forward: $fwd_regex.\n",
+#                  "##$count_fwd_regex on the forward strand.\n",
+#                  "##$seq_tally sequences.  Mean motifs per seq = $mean\n");
+#
+   print STDOUT "There were $count_fwd_regex instances of $fwd_regex on the forward strand.\n"; 
+}
+
+$output->close;
+
+exit;
+
+sub iupac2regex {
+# Convert IUPAC codes to REGEX
+   my $iupac = shift;
+   
+   #### Series of regexes to convert 
+   if($iupac =~ /A/) { return 'A' }
+   if($iupac =~ /C/) { return 'C' }
+   if($iupac =~ /G/) { return 'G' }
+   if($iupac =~ /T/) { return 'T' }
+   if($iupac =~ /M/) { return '[AC]' }
+   if($iupac =~ /R/) { return '[AG]' }
+   if($iupac =~ /W/) { return '[AT]' }
+   if($iupac =~ /S/) { return '[CG]' }
+   if($iupac =~ /Y/) { return '[CT]' }
+   if($iupac =~ /K/) { return '[GT]' }
+   if($iupac =~ /V/) { return '[ACG]' }
+   if($iupac =~ /H/) { return '[ACT]' }
+   if($iupac =~ /D/) { return '[AGT]' }
+   if($iupac =~ /B/) { return '[CGT]' }
+   if($iupac =~ /N/) { return '[ACGT]' }
+
+   die("IUPAC not recognised by sub iupac2regex!\n");
+}
+
+sub RevCompIUPAC {
+   my $iupac_string = shift;
+   my @converted_list = ();
+
+   my @iupac_string_list = split(//, $iupac_string); 
+
+   @iupac_string_list = reverse(@iupac_string_list);
+
+   foreach my $letter (@iupac_string_list) {
+      $letter =~ tr/ACGTRYMKWSBDHVN/TGCAYRKMWSVHDBN/;
+      push(@converted_list, $letter);
+   }
+
+   my $joined_list = join('', @converted_list);
+   return $joined_list;
+}